Clustal Omega
Developer(s) Des Higgins, Fabian Sievers, David Dineen, and Andreas Wilm (all at the Conway Institute, UCD)
Stable release 1.2.0 / 12 June 2013; 12 months ago (2013-06-12)
Written in C++
Operating system UNIX, Linux, Mac, MS-Windows
Type Bioinformatics tool
Licence Free for academic users
Developer(s) Gibson T. (EMBL), Thompson J. (CNRS), Higgins D. (UCD)
Stable release 2.1 / 17 November 2010; 3 years ago (2010-11-17)
Written in C++
Operating system UNIX, Linux, Mac, MS-Windows
Type Bioinformatics tool
Licence GNU Lesser General Public License [1]

Clustal is a widely used multiple sequence alignment computer program.[2] There are three main variations:

  • ClustalW: command line interface[3]
  • ClustalX: This version has a graphical user interface.[4]
  • Clustal Omega: Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours. It will also make use of multiple processors, where present. In addition, the quality of alignments is superior to previous versions, as measured by a range of popular benchmarks. (Note: Command line-only, protein-only program.)[5]

All three are available for Windows, Mac OS, and Unix/Linux.

This program is available from the European Bioinformatics Institute ftp server.


This program accepts a wide range of input formats, including NBRF/PIR, FASTA, EMBL/Swiss-Prot, Clustal, GCC/MSF, GCG9 RSF, and GDE.

The output format can be one or many of the following: Clustal, NBRF/PIR, GCG/MSF, PHYLIP, GDE, or NEXUS.

Multiple sequence alignment

There are three main steps:

  1. Do a pairwise alignment
  2. Create a guide tree (or use a user-defined tree)
  3. Use the guide tree to carry out a multiple alignment

These are done automatically when you select "Do Complete Alignment". Other options are "Do Alignment from guide tree" and "Produce guide tree only".


Users can align the sequences using the default setting, but occasionally it may be useful to customize one's own parameters.

The main parameters are the gap opening penalty, and the gap extension penalty.


The guide tree in the initial programs was constructed via a UPGMA cluster analysis of the pairwise alignments, hence the name CLUSTAL.[6]cf.[7] The first four versions in 1988 had arabic numerals (1 to 4), whereas with the fifth version Des Higgins switched to roman numeral V in 1992.[6]cf.[8][9] In 1994 and in 1997, for the next two versions, the letters after the letter V were used and made to correspond to W for Weighted and X for X Window.[6]cf.[10][11] The name omega was chosen to mark a change from the previous ones.[6]

See also


External links

  • Clustal Homepage (free Unix/Linux, Mac, and Windows download)
  • ClustalW and ClustalX mirror at the EBI (free Unix/Linux, Mac, and Windows download)
  • "Accelerating Intensive Applications at 10x-50x Speedup to Remove Bottlenecks in Computational Workflows" — White Paper by Progeniq Pte Ltd.
  • Multiple Sequence Alignment by CLUSTALW
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